[med-svn] r19557 - in trunk/packages/hyphy/trunk/debian: . patches source
Andreas Tille
tille at moszumanska.debian.org
Tue Jul 7 12:48:14 UTC 2015
Author: tille
Date: 2015-07-07 12:48:14 +0000 (Tue, 07 Jul 2015)
New Revision: 19557
Added:
trunk/packages/hyphy/trunk/debian/hyphy-common.install
trunk/packages/hyphy/trunk/debian/hyphy-common.links
trunk/packages/hyphy/trunk/debian/hyphy-mpi.install
trunk/packages/hyphy/trunk/debian/hyphy.install
trunk/packages/hyphy/trunk/debian/patches/
trunk/packages/hyphy/trunk/debian/patches/arch_all_files_to_usr_share.patch
trunk/packages/hyphy/trunk/debian/patches/series
trunk/packages/hyphy/trunk/debian/source/lintian-overrides
Modified:
trunk/packages/hyphy/trunk/debian/control
trunk/packages/hyphy/trunk/debian/rules
Log:
Split into several binary packages and lintian polishing
Modified: trunk/packages/hyphy/trunk/debian/control
===================================================================
--- trunk/packages/hyphy/trunk/debian/control 2015-07-07 07:59:20 UTC (rev 19556)
+++ trunk/packages/hyphy/trunk/debian/control 2015-07-07 12:48:14 UTC (rev 19557)
@@ -17,7 +17,7 @@
Package: hyphy
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, hyphy-common
Description: Hypothesis testing using Phylogenies
HyPhy is an open-source software package for the analysis of genetic
sequences using techniques in phylogenetics, molecular evolution, and
@@ -28,3 +28,36 @@
library and called from other programming environments such as Python or
R. Continued development of HyPhy is currently supported in part by an
NIGMS R01 award 1R01GM093939.
+
+Package: hyphy-mpi
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, hyphy-common
+Description: Hypothesis testing using Phylogenies (MPI version)
+ HyPhy is an open-source software package for the analysis of genetic
+ sequences using techniques in phylogenetics, molecular evolution, and
+ machine learning. It features a complete graphical user interface (GUI)
+ and a rich scripting language for limitless customization of analyses.
+ Additionally, HyPhy features support for parallel computing environments
+ (via message passing interface) and it can be compiled as a shared
+ library and called from other programming environments such as Python or
+ R. Continued development of HyPhy is currently supported in part by an
+ NIGMS R01 award 1R01GM093939.
+ .
+ This package provides the MPI version.
+
+Package: hyphy-common
+Suggests: hyphy | hyphy-mpi
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Hypothesis testing using Phylogenies (common files)
+ HyPhy is an open-source software package for the analysis of genetic
+ sequences using techniques in phylogenetics, molecular evolution, and
+ machine learning. It features a complete graphical user interface (GUI)
+ and a rich scripting language for limitless customization of analyses.
+ Additionally, HyPhy features support for parallel computing environments
+ (via message passing interface) and it can be compiled as a shared
+ library and called from other programming environments such as Python or
+ R. Continued development of HyPhy is currently supported in part by an
+ NIGMS R01 award 1R01GM093939.
+ .
+ This package provides files that are common to all binary versions.
Added: trunk/packages/hyphy/trunk/debian/hyphy-common.install
===================================================================
--- trunk/packages/hyphy/trunk/debian/hyphy-common.install (rev 0)
+++ trunk/packages/hyphy/trunk/debian/hyphy-common.install 2015-07-07 12:48:14 UTC (rev 19557)
@@ -0,0 +1 @@
+usr/lib/* usr/share
Added: trunk/packages/hyphy/trunk/debian/hyphy-common.links
===================================================================
--- trunk/packages/hyphy/trunk/debian/hyphy-common.links (rev 0)
+++ trunk/packages/hyphy/trunk/debian/hyphy-common.links 2015-07-07 12:48:14 UTC (rev 19557)
@@ -0,0 +1 @@
+usr/share/hyphy usr/lib/hyphy
Added: trunk/packages/hyphy/trunk/debian/hyphy-mpi.install
===================================================================
--- trunk/packages/hyphy/trunk/debian/hyphy-mpi.install (rev 0)
+++ trunk/packages/hyphy/trunk/debian/hyphy-mpi.install 2015-07-07 12:48:14 UTC (rev 19557)
@@ -0,0 +1 @@
+usr/bin/*mpi
Added: trunk/packages/hyphy/trunk/debian/hyphy.install
===================================================================
--- trunk/packages/hyphy/trunk/debian/hyphy.install (rev 0)
+++ trunk/packages/hyphy/trunk/debian/hyphy.install 2015-07-07 12:48:14 UTC (rev 19557)
@@ -0,0 +1 @@
+usr/bin/*gtk
Added: trunk/packages/hyphy/trunk/debian/patches/arch_all_files_to_usr_share.patch
===================================================================
--- trunk/packages/hyphy/trunk/debian/patches/arch_all_files_to_usr_share.patch (rev 0)
+++ trunk/packages/hyphy/trunk/debian/patches/arch_all_files_to_usr_share.patch 2015-07-07 12:48:14 UTC (rev 19557)
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 29 Jun 2015 11:13:57 +0200
+Description: Move arch all files to /usr/share
+ Deactivated since it does not work this way
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -277,7 +277,7 @@ target_link_libraries(hyphy_mp ${DEFAULT
+
+ install(
+ TARGETS hyphy_mp
+- LIBRARY DESTINATION lib
++ LIBRARY DESTINATION share
+ OPTIONAL
+ )
+
Added: trunk/packages/hyphy/trunk/debian/patches/series
===================================================================
--- trunk/packages/hyphy/trunk/debian/patches/series (rev 0)
+++ trunk/packages/hyphy/trunk/debian/patches/series 2015-07-07 12:48:14 UTC (rev 19557)
@@ -0,0 +1 @@
+# arch_all_files_to_usr_share.patch
Modified: trunk/packages/hyphy/trunk/debian/rules
===================================================================
--- trunk/packages/hyphy/trunk/debian/rules 2015-07-07 07:59:20 UTC (rev 19556)
+++ trunk/packages/hyphy/trunk/debian/rules 2015-07-07 12:48:14 UTC (rev 19557)
@@ -16,10 +16,15 @@
./obj-$(DEB_TARGET_GNU_TYPE)/HYPHYGTEST
override_dh_install:
- dh_install
# smallcaps for executables
for bindir in `find . -type d -name bin` ; do \
for bin in $${bindir}/* ; do \
- ln -s `basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \
+ # ln -s `basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \
+ mv $${bindir}/`basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \
done ; \
done
+ dh_install
+ # remove some junk that should not even be in the source tarball
+ find debian -name .DS_Store -delete
+ find debian -name .xvpics -delete
+ find debian -name ..gtkrc.swp
Added: trunk/packages/hyphy/trunk/debian/source/lintian-overrides
===================================================================
--- trunk/packages/hyphy/trunk/debian/source/lintian-overrides (rev 0)
+++ trunk/packages/hyphy/trunk/debian/source/lintian-overrides 2015-07-07 12:48:14 UTC (rev 19557)
@@ -0,0 +1,4 @@
+# These files are not used anyway
+hyphy source: outdated-autotools-helper-file contrib/gtest-1.7.0/build-aux/config.sub 2012-02-10
+hyphy source: outdated-autotools-helper-file contrib/gtest-1.7.0/build-aux/config.guess 2012-02-10
+
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